4RIT

The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

Wu, R.Clancy, S.Joachimiak, A.Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal-dependent decarboxylase
B, A
486Sphaerobacter thermophilus (strain DSM 20745 / S 6022)Mutation(s): 0 
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022))
Go to UniProtKB:  D1C7D8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.483α = 90.00
b = 118.566β = 90.00
c = 126.018γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release